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| Ulrich Bodenhofer; Andreas Kothmeier; Ingrid G. Abfalter; Carsten C. Mahrenholz; Sepp Hochreiter. |
| Classifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obtaining a highly accurate classifier is rarely the end of the story in many practical situations. Instead, one often aims to acquire biological knowledge about the principles underlying a given classification task. SVMs with traditional sequence kernels do not offer a straightforward way of accessing this knowledge.

In this contribution, we propose a new approach to analyzing... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4708/version/1 |
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| Carsten C. Mahrenholz*; Ingrid G. Abfalter*; Ulrich Bodenhofer; Rudolf Volkmer; Sepp Hochreiter. |
| *Overview* | Coiled coils are usually described as consisting of two up to seven α-helices that are wrapped around each other. They can associate as either homomeric or heteromeric structures and bind in parallel or antiparallel topologies. Another characteristic of all coiled coils is the periodic recurrence of a sequence [abcdefg]n called heptad repeat, where n denotes the heptad number. In these repeats, a and d are hydrophobic amino acids at core positions crucial for the tertiary structure. In contrast, the polar positions b, c, and f are hydrophilic and e and g are charged residues.
Due to their ability to oligomerize, coiled coils are involved in a variety of important cellular functions, either on their own or as part of... |
| Tipo: Poster |
Palavras-chave: Chemistry; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4677/version/1 |
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| Günter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter. |
| Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4710/version/1 |
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| Andreas Mayr; Djork-Arne Clevert; Sepp Hochreiter. |
| One of the main topics in systems biology is to model genetic pathways. Genes of a pathway, which show linear dependencies of their expression values, are easy to identify to belong to the pathway. However, if feedback loops or signal cascades are present, gene expression values of pathway genes can be nonlinearly dependent on the expression values of other genes in the pathway. In this situation such genes are hard to detect as belonging to the pathway because nonlinearity and noise must be distinguished.

We propose an algorithm to infer nonlinear network elements in pathways from microarray data. Our model assumes, that gene expression values, belonging to one pathway, are mainly driven by one single latent factor. We... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4715/version/1 |
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| Karin Schwarzbauer; Günter Klambauer; Andreas Mayr; Sepp Hochreiter. |
| Next generation sequencing (NGS) technologies have profoundly impacted biological research and are becoming more and more popular due to cost effectiveness and their speed. NGS can be utilized to identify DNA structural variants, namely copy number variations (CNVs) which showed association with diseases like HIV, diabetes II, or cancer.

There have been first approaches to detect CNVs in NGS data, where most of them detect a CNV by a significant difference of read counts within neighboring windows at the chromosome. However these methods suffer from systematical variations of the underlying read count distributions along the chromosome due to biological and technical noise. In contrast to these global methods, we locally... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4716/version/1 |
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| Günter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter. |
| Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Molecular Cell Biology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4710/version/2 |
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